Difference between revisions of "FASTA"
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Moskalenko (talk | contribs) m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
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|{{#vardefine:app|fasta}} | |{{#vardefine:app|fasta}} | ||
|{{#vardefine:url|http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml}} | |{{#vardefine:url|http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml}} | ||
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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FASTA can be used to infer functional and evolutionary relationships between | FASTA can be used to infer functional and evolutionary relationships between | ||
sequences as well as help identify members of gene families. | sequences as well as help identify members of gene families. | ||
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<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | == | + | ==System Variables== |
| − | *{{#var:app}} | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_FASTA_BIN - executable directory | * HPC_FASTA_BIN - executable directory | ||
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==Available documentation== | ==Available documentation== | ||
Several man pages are available: | Several man pages are available: | ||
* fasta3, fastf3, fasts3, map_db, prss3, pvcomp | * fasta3, fastf3, fasts3, map_db, prss3, pvcomp | ||
Type "man MANPAGE" to access them at the command line. | Type "man MANPAGE" to access them at the command line. | ||
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{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
Latest revision as of 18:54, 12 August 2022
Description
The FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
Environment Modules
Run module spider fasta to find out what environment modules are available for this application.
System Variables
- HPC_FASTA_DIR - installation directory
- HPC_FASTA_BIN - executable directory
Available documentation
Several man pages are available:
- fasta3, fastf3, fasts3, map_db, prss3, pvcomp
Type "man MANPAGE" to access them at the command line.